Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nr4a1

Cell type

Cell type Class
Blood
Cell type
Treg
NA
NA

Attributes by original data submitter

Sample

source_name
Regulatory T (Treg) cells
cell type
Regulatory T cells
tissue
spleens and lymph nodes
strain
C57BL/6
chip antibody
anti-NR4A1 antibody, clone H1648 (Perseus Proteomics, catalog# PP-H1648-00, lot# A-1)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and Nr4a1-DNA complexes were isolated with antibody (anti-NR4A1 antibody, clone H1648, cat#PP-H1648-00, lot#A-1, Perseus Proteomics). Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Cat# IP-202-1012). Briefly, DNA was end-repaired, then protruding 3- 'A' bases were ligated to Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 250~350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation, using TruSeq SR Cluster Kit vs-cBot-HS (Cat#GD-401-3001). Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols, Using TruSeq SBS Kit v3-HS (Cat#FC-401-3002).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
28962847
Reads aligned (%)
91.2
Duplicates removed (%)
77.0
Number of peaks
500 (qval < 1E-05)

mm9

Number of total reads
28962847
Reads aligned (%)
91.0
Duplicates removed (%)
77.2
Number of peaks
517 (qval < 1E-05)

Base call quality data from DBCLS SRA